[Insight-users] rat brain atlas based VOIs

[Stephen R. Aylward]

Another option - use the landmarkinitializedmutualinformationapplication 
to register the MR and the histological images.   This was what we did 
for the image shown in this link:

http://caddlab.rad.unc.edu/projects/RodentAtlas/Rat-MR-Atlas-small.gif

The problem is that there is currently a bug in the program when doing 
affine registration - I should have a fix checked-in in a few days.

Note that using the advanced options, you can specify a region of 
interest for the registration - that way the inter-rodent registration 
can focus on the brain and ignore the other differences.   We've had 
quite good luck with it.

Stephen

raghu venkatram wrote:

> Hello ITKers,
>  
> I was wondering if anybody had defined/created VOI's volumes of interest 
> for the rat brain using ITK for certain structures based on paxinos rat 
> brain atlas. It would be really helpful, if I could get to use these.
>  
> I am trying to segment out rat brain structures and define 3d 
> VOIs(volumes of interest), I am using the paxinos wire frame atlas. This 
> atlas has the annotated regions and basically the slices are bitmaps. 
> There is no segmentation per se but regrouping of regions to form whole 
> brain structures and labelling them.
>  
> I would be glad if anybody had suggestions on this.
>  
> I intend to use these 3d VOI's/ structures to perform 
> template segmentation on PET and MR images of the rat brain later on.
>  
> Thank you,
>  
> Raghu Venkatram
> 
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-- 
===========================================================
Dr. Stephen R. Aylward
Associate Professor of Radiology
Adjunct Associate Professor of Computer Science and Surgery
http://caddlab.rad.unc.edu
aylward at unc.edu
(919) 966-9695